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[REVIEW]: DiffOpt: Parallel optimization of Jax models #7522

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editorialbot opened this issue Nov 24, 2024 · 59 comments
Closed

[REVIEW]: DiffOpt: Parallel optimization of Jax models #7522

editorialbot opened this issue Nov 24, 2024 · 59 comments
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accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning

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editorialbot commented Nov 24, 2024

Submitting author: @AlanPearl (Alan Pearl)
Repository: https://github.com/AlanPearl/diffopt
Branch with paper.md (empty if default branch): paper
Version: v1.1.1
Editor: @jbytecode
Reviewers: @landreman, @ewu63
Archive: 10.5281/zenodo.14291795

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/211b25a3f9df01ca85be7100ad149e87"><img src="https://joss.theoj.org/papers/211b25a3f9df01ca85be7100ad149e87/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/211b25a3f9df01ca85be7100ad149e87/status.svg)](https://joss.theoj.org/papers/211b25a3f9df01ca85be7100ad149e87)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@landreman & @ewu63, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @jbytecode know.

Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest

Checklists

📝 Checklist for @landreman

📝 Checklist for @ewu63

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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1131.6 files/s, 181175.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          23            532            805           1893
Jupyter Notebook                 5              0           1789            782
Markdown                         2             36              0            165
TeX                              1              6              0             86
YAML                             3              6              4             59
reStructuredText                 3             48             54             50
TOML                             1              5              0             29
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            40            645           2660           3099
-------------------------------------------------------------------------------

Commit count by author:

    17	Alan Pearl

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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.21105/astro.2105.05859 is OK
- 10.1093/mnras/stac3118 is OK
- 10.1093/mnras/stad456 is OK
- 10.1109/ICNN.1995.488968 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Multivariate Density Estimation
- No DOI given, and none found for title: Mathematical methods of statistics

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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Paper file info:

📄 Wordcount for paper.md is 1259

✅ The paper includes a Statement of need section

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License info:

✅ License found: MIT License (Valid open source OSI approved license)

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@jbytecode
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Dear Reviewers @landreman and @ewu63

You can start by creating your task lists. Each list will contain several tasks.

As you complete each task, you can check off the corresponding checkbox. Since the review process for JOSS is interactive, you are encouraged to engage with the author, other reviewers, and the editor throughout. You can open issues and submit pull requests in the target repository. Please include the URL of this page in those interactions, so we can keep track of activities outside of the platform.

To generate your task list, simply type:

@editorialbot generate my checklist

Thank you in advance.

@landreman
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landreman commented Nov 24, 2024

Review checklist for @landreman

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/AlanPearl/diffopt?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@AlanPearl) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1. Contribute to the software 2. Report issues or problems with the software 3. Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@ewu63
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ewu63 commented Nov 26, 2024

Review checklist for @ewu63

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/AlanPearl/diffopt?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@AlanPearl) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • Community guidelines: Are there clear guidelines for third parties wishing to 1. Contribute to the software 2. Report issues or problems with the software 3. Seek support

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

@landreman
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@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@landreman
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All the items in the checklist are complete so I approve the paper for publication. Is there anything more I need to do to sign off?

@jbytecode
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@landreman - Thank you for your review. By now, nothing to do in your side. Whenever we get the final action from the other reviewer, I'll start my editorial stuff.

@ewu63
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ewu63 commented Dec 5, 2024

I am also finished with the review and checked all items off.

@jbytecode
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jbytecode commented Dec 5, 2024

@ewu63 - Don't you have any additional suggestions/corrections or something else? Could you provide me a brief reviewer report with 3-4 sentences? I am writing this post because it seems you haven't presented any counter ideas and suggestions and it looks like your decision is to accept as is, right?

@ewu63
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ewu63 commented Dec 6, 2024

@jbytecode the only comment I had was here regarding references. The main module of the library, multigrad, propagates jax-computed Jacobians under MPI, and is used by kdescent to perform stochastic gradient descent. multiswarm on the other hand implements a parallel PSO algorithm, which is neither novel in theory nor in implementation. However, while similar capabilities can be obtained via established libraries such as mpi4jax, this library does offer some conveniences in providing wrappers for specific applications such as running adam, and has been used to produce published results in astrophysics.
I have locally installed the package and verified that the examples/tests run and achieve the speedups claimed in the paper, and the tutorials/documentation are well written. The paper itself is also well written and I recommend this paper for publication as is.

@jbytecode
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@ewu63 - Thank you for the clarification.

@jbytecode
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jbytecode commented Dec 6, 2024

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

  • Double check authors and affiliations (including ORCIDs)
  • Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
  • Archive the release on Zenodo/figshare/etc and post the DOI here.
  • Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
  • Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

  • Read the text of the paper and offer comments/corrections (as either a list or a pull request)
  • Check that the archive title, author list, version tag, and the license are correct
  • Set archive DOI with @editorialbot set <DOI here> as archive
  • Set version with @editorialbot set <version here> as version
  • Double check rendering of paper with @editorialbot generate pdf
  • Specifically check the references with @editorialbot check references and ask author(s) to update as needed
  • Recommend acceptance with @editorialbot recommend-accept

@AlanPearl
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Done. Here is the requested info:

@jbytecode
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@AlanPearl - The metadata of manuscript should match those in the Zenodo archive, please add contributors to the authors list with the proper information including their DOIs. Thank you in advance.

@jbytecode
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@editorialbot set v1.1.1 as version

@jbytecode
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@AlanPearl - The manuscript looks almost perfect. I've just sent a pull request that includes minor fixes in both the manuscript and the bibliography (AlanPearl/diffopt#7). Please review the PR, if you're okay with them, please merge.
Thank you in advance.

@jbytecode
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@editorialbot check references

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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.21105/astro.2105.05859 is OK
- 10.1093/mnras/stac3118 is OK
- 10.1093/mnras/stad456 is OK
- 10.2307/1270280 is OK
- 10.1109/ICNN.1995.488968 is OK
- 10.21105/joss.03419 is OK
- 10.1007/s00158-019-02211-z is OK
- 10.1109/PACRIM.2005.1517282 is OK
- 10.1109/access.2020.2990567 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Mathematical methods of statistics

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

@jbytecode
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@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@jbytecode
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@AlanPearl - The manuscript looks good to me. Please perform a full read of the paper and fix any thing if you think it's wrong. Please tell me when you've done with them. Thank you in advance.

@AlanPearl
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@jbytecode Okay I have finished my final reading, and it looks good to me.

@jbytecode
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@editorialbot check references

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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.21105/astro.2105.05859 is OK
- 10.1093/mnras/stac3118 is OK
- 10.1093/mnras/stad456 is OK
- 10.2307/1270280 is OK
- 10.1109/ICNN.1995.488968 is OK
- 10.21105/joss.03419 is OK
- 10.1007/s00158-019-02211-z is OK
- 10.1109/PACRIM.2005.1517282 is OK
- 10.1109/access.2020.2990567 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Mathematical methods of statistics

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

@jbytecode
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@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@jbytecode
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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.21105/astro.2105.05859 is OK
- 10.1093/mnras/stac3118 is OK
- 10.1093/mnras/stad456 is OK
- 10.2307/1270280 is OK
- 10.1109/ICNN.1995.488968 is OK
- 10.21105/joss.03419 is OK
- 10.1007/s00158-019-02211-z is OK
- 10.1109/PACRIM.2005.1517282 is OK
- 10.1109/access.2020.2990567 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: JAX: composable transformations of Python+NumPy pr...
- No DOI given, and none found for title: Mathematical methods of statistics

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

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👋 @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6261, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 17, 2024
@crvernon
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crvernon commented Dec 20, 2024

@editorialbot generate pdf

🔍 checking out the following:

  • reviewer checklists are completed or addressed
  • version set
  • archive set
  • archive names (including order) and title in archive matches those specified in the paper
  • archive uses the same license as the repo and is OSI approved as open source
  • archive DOI and version match or redirect to those set by editor in review thread
  • paper is error free - grammar and typos
  • paper is error free - test links in the paper and bib
  • paper is error free - refs preserve capitalization where necessary
  • paper is error free - no invalid refs without justification

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@crvernon
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@editorialbot accept

Very clean paper. Thank you!

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Doing it live! Attempting automated processing of paper acceptance...

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Pearl
  given-names: Alan N.
  orcid: "https://orcid.org/0000-0001-9820-9619"
- family-names: Beltz-Mohrmann
  given-names: Gillian D.
  orcid: "https://orcid.org/0000-0002-4392-8920"
- family-names: Hearin
  given-names: Andrew P.
  orcid: "https://orcid.org/0000-0003-2219-6852"
doi: 10.5281/zenodo.14291795
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Pearl
    given-names: Alan N.
    orcid: "https://orcid.org/0000-0001-9820-9619"
  - family-names: Beltz-Mohrmann
    given-names: Gillian D.
    orcid: "https://orcid.org/0000-0002-4392-8920"
  - family-names: Hearin
    given-names: Andrew P.
    orcid: "https://orcid.org/0000-0003-2219-6852"
  date-published: 2024-12-20
  doi: 10.21105/joss.07522
  issn: 2475-9066
  issue: 104
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7522
  title: "DiffOpt: Parallel optimization of Jax models"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07522"
  volume: 9
title: "DiffOpt: Parallel optimization of Jax models"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

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🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.07522 joss-papers#6277
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07522
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Dec 20, 2024
@crvernon
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🥳 Congratulations on your new publication @AlanPearl ! Many thanks to @jbytecode for editing and @landreman and @ewu63 for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

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🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following

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  <img src="https://joss.theoj.org/papers/10.21105/joss.07522/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07522/status.svg
   :target: https://doi.org/10.21105/joss.07522

This is how it will look in your documentation:

DOI

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